New Genes for Old Functions

Larry Fiddick asked a few weeks ago what we most want to know concerning
genetics and evolution. I'm curious about a subject that could be called
"New Genes for Old Functions". How commonly genes are replaced by
non-orthologous genes over evolutionary time, and what evolutionary
process(es) is(are) responsible for this? What I mean by this is probably
unclear, so I'll supply some examples:
example 1. The abalone _S. diversicolor aquatilis_ has an heme-binding
oxygen carrier concentrated in its buccal mass. Functionally this molecule
is a myoglobin, yet the amino acid sequence reveals a specific relationship
to the heme-binding enzyme indoleamine 2,3-dioxygenase, and no detectable
relationship to the globin family (hemoglobins, myoglobins, leghemoglobins
& various globin-related proteins in microbes). [see Suzuki & Takagi,
1992, J. Mol. Biol. 228: 698]
example 2. Maeda & Fitch (1982, J.B.C. 257: 2806) isolated a presumptive
myoglobin from bullfrog heart muscle. The sequence shows homology to the
globin family, yet this molecule (functionally a myoglobin) is more closely
related to hemoglobin chains (specifically, to alpha chains) than to
myoglobin chains.
example 3. the trpE & trpG genes of eubacteria are part of a larger family
of homologous synthetase/amidotransferase enzyme pairs that function not
only in the tryptophan pathway (trpE & G), but also in the folate pathway
(pabB & A). Curiously, the trpE & trpG genes of fluorescent pseudomonads
are more closely related to the pabB & pabA genes (folate pathway) of
enterics than to their trpE & trpG genes (trp pathway) [see Crawford &
Milkman's chapter in _Evolution at the Molecular Level_, Sinauer, ca.
1991].
Each case evokes a phenomenon in which a gene encoding a particular
function is replaced with an analogous gene ['analogous' means 'having a
similar function']. In examples #2 and #3, the analogous genes are also
homologous genes that are recognized as different because they are part of
a paralogous gene family ['paralogous' means 'evolutionarily related _via_
an ancestral gene duplication'], but in example #1 it is not even
detectably homologous.
Crawford and Milkman suggest that the gene replacement process is initiated
with conditions in which a function becomes superfluous (so that the
original gene can be lost) and that the process is completed with
gradually-arising conditions in which the function becomes more & more
useful, providing a stimulus for the population to either "improvise" or
"import". Improvisation would mean modifying a non-homologous or
paralogous in-house gene (e.g., the case of fluorescent pseudomonad trp
genes), and 'import' would mean gaining a 'xenologous' [Fitch's term, I
believe] gene by lateral transfer (e.g., there is a clear case of lateral
transfer of an entire trp operon from an enteric bacterial source to the
gram positive bacterium _Brevibacterium lactofermentum_, as discussed by
Milkman & Crawford).
The relevant questions are (I suppose):
1. How commonly are genes replaced by paralogous or even non-homologous
genes? For every case that is easy to detect because the paralogous or
xenologous genes are so obviously distinct, are there dozens or hundreds of
cases in which a gene replacment just makes a minor departure from the
expectations of orthology, and therefore undermines the congruence of
traits without being itself detectable? Are some genes immune (or less
subject) to this process, for whatever reason?
2. What is(are) the mechanism(s)? Is lateral transfer (i.e., gain of a
xenologous gene) an alternative outcome of the same mechanism, as suggested
by Milkman & Crawford? Does the original gene have to be lost? One can
imagine a bacterium losing trp genes under conditions of plentiful
environmental tryptophan, and our knowledge of bacterial genetics supplies
us with many clues as to how a bacterium might improvise or import to
compensate its loss (e.g., the _ebg_ locus of E. coli; broad-host range
plasmids carrying a cornucopia of diverse genes). A tetrapod could
improvise with genes, too, but how could it have gone through a stage
lacking heart myoglobin?
Arlin